diff --git a/src/chipster.nf b/src/chipster.nf index b900127f3d1ae71006ed61b392e357252e26c0a8..931935e3902c32220c87fd4384bf0c641b7df0ef 100755 --- a/src/chipster.nf +++ b/src/chipster.nf @@ -152,9 +152,6 @@ include { index_bam } from "./nf_modules/samtools/main.nf" include { bam_to_bigwig } from "./nf_modules/deeptools/main.nf" include { chipseq_bam2BG } from "./nf_modules/deeptools/main.nf" include { peak_calling_bg } from "./nf_modules/macs3/main.nf" -include { bam_to_bed } from "./nf_modules/bedtools/main.nf" -include { bed_slop } from "./nf_modules/bedtools/main.nf" -include { bed_to_bedGraph } from "./nf_modules/bedtools/main.nf" /* **************************************************************** @@ -184,7 +181,7 @@ workflow { // mapping preprocessed reads mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq) - /*if (!params.idxgenome) { + /*if (params.idxgenome == "") { index_fasta(genome_file) mapping_fastq(index_fasta.out.index.collect(), fastp_default.out.fastq) } else { @@ -207,15 +204,6 @@ workflow { // Chipseq Bam 2 bigwig file with reads extends chipseq_bam2BG(index_bam.out.bam_idx) - // From Bam to Bed - // bam_to_bed(sort_bam.out.bam) - - // Extension of reads with bedtools slop - // bed_slop(bam_to_bed.out.bed, genome_sizes.collect()) - - // From bed to bedgraph - // bed_to_bedGraph(bed_slop.out, genome_sizes.collect()) - // peak calling using MACS3 Prend des bed ou des bam en entrée... // peak_calling_bg() } \ No newline at end of file diff --git a/src/test.nf b/src/test.nf new file mode 100644 index 0000000000000000000000000000000000000000..be6c7083286ee4bcd8d048a875ff52b83131780b --- /dev/null +++ b/src/test.nf @@ -0,0 +1,16 @@ +nextflow.enable.dsl=2 + + +Channel + .from([[1, "fastq1.fq"], [2, "fastq2.fq"], [3, "fastq3.fq"], [4, "fastq4.fq"]]) + .set{ fastq_files } + +Channel + .from([[1, "test"], [2, "test"], [3, "ctrl"], [4, "ctrl"]]) + .set { sample_names } + + +// fastq_files.join(sample_names).map{it -> [file(it[1]).baseName, it[1], it[2]]}.view() +fastq_files.join(sample_names).set{ vals } + +vals.combine(vals).filter { it -> (it[2] != it[5]) && (it[2] == "test") }.view() \ No newline at end of file